6T6G

Bacteroides salyersiae GH164 beta-mannosidase in complex with noeuromycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6T5O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M ammonium tartrate pH 7.0, 13 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5952.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.754α = 92.602
b = 105.096β = 97.209
c = 170.544γ = 105.096
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.916DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.06101.1398.30.9865.23.5280992
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.10.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6T5O2.0690.1912809851397198.2280.2140.21220.239944.862
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.7550.496-0.979-0.0930.21-1.595
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.764
r_dihedral_angle_4_deg24.434
r_dihedral_angle_3_deg16.356
r_dihedral_angle_1_deg7.739
r_lrange_it5.166
r_lrange_other5.158
r_scangle_it3.123
r_scangle_other3.123
r_mcangle_it2.875
r_mcangle_other2.875
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.764
r_dihedral_angle_4_deg24.434
r_dihedral_angle_3_deg16.356
r_dihedral_angle_1_deg7.739
r_lrange_it5.166
r_lrange_other5.158
r_scangle_it3.123
r_scangle_other3.123
r_mcangle_it2.875
r_mcangle_other2.875
r_scbond_it1.879
r_scbond_other1.879
r_mcbond_it1.799
r_mcbond_other1.799
r_angle_refined_deg1.613
r_angle_other_deg1.368
r_nbd_other0.239
r_nbd_refined0.204
r_symmetry_nbd_other0.189
r_symmetry_xyhbond_nbd_refined0.184
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.148
r_symmetry_nbd_refined0.125
r_chiral_restr_other0.081
r_symmetry_nbtor_other0.081
r_chiral_restr0.08
r_ncsr_local_group_100.079
r_ncsr_local_group_40.078
r_ncsr_local_group_130.075
r_ncsr_local_group_140.075
r_ncsr_local_group_20.074
r_ncsr_local_group_80.074
r_ncsr_local_group_10.073
r_ncsr_local_group_30.073
r_ncsr_local_group_50.073
r_ncsr_local_group_90.073
r_ncsr_local_group_120.073
r_ncsr_local_group_150.073
r_ncsr_local_group_70.072
r_ncsr_local_group_60.071
r_ncsr_local_group_110.071
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms31476
Nucleic Acid Atoms
Solvent Atoms1029
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
xia2data scaling
PHASERphasing